Sequencing of ancient genomes from southern Africa — helps in estimating modern human divergence between 350K and 260K years ago

As discussed many times on these GEITP pages –– archaeological, fossil, and genetic data have positioned the early traces of anatomically modern humans in sub-Saharan Africa. The earliest (completely) modern human remains, dating to ~190,000 years ago, originate from Ethiopia. Fossils displaying some features of early anatomical modernism from Morocco are dated to ~315,000 years ago. Southern Africa has been occupied by the Homo genus (and more than 20 sublines, or species) from about 2 million years ago, with a major transitional phase from the Early Stone Age to the Middle Stone Age, between 600,000 and 200,000 years ago.

Fossil records indicate the presence of archaic Homo sapiens at more than 200,00 years ago and anatomically modern humans from ~120,000 years ago. Whole-genome sequencing (WGS) studies have identified southern African Khoe-San populations as carrying more unique DNA variants and more divergent lineages than other living groups –– consistent with being among the oldest tribes that still exist (partially) intact on the planet. The deepest population split among modern humans — between Khoe-San and other groups — was estimated to be ~160,000 to 100,000 years ago on the basis of short-sequence fragments and genome-wide single-nucleotide polymorphism data. These estimates have now been re-scaled to range between 250,000 and 300,000 years ago after revisions of the human mutation rate from pedigrees.

Genetic variation in the Khoe-Sanwas was used previously to argue for a southern African origin of modern humans, although multiple regions in Africa have also been proposed. Middle Stone Age sites in KwaZulu-Natal (South Africa) demonstrate human occupation since more than 100,000 years ago. Authors [see attached paper] report on the genomes of seven ancient individuals from KwaZulu-Natal. They sequenced three Stone Age hunter-gatherers and four Iron Age farmers, dated to ~2,000, and 5000 to 3000 years ago, respectively. Genome-sequencing coverage was between 0.01x and 13.2x. The data displayed characteristics of ancient DNA –– the remains of the three Stone Age hunter-gatherers (~2000 years old) were genetically similar to current-day southern San groups, and those of the four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. Authors estimated that all modern-day Khoe-San groups have been influenced by 9% to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, they estimated the first modern human population divergence time to be between 350,000 and 260,000 years ago; this estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.